Hi loryc  Welcome to CLF!
I don't think 6 pair of shoes are too many for a Med cruise, but you'll probably get the most use out of your walking shoes in the ports. Remember a lot of the streets are cobblestone so good walking shoes are a must! Also, there is a lot of walking and possibly climbing stairs being done
I was in the Med in November so the weather was a bit cooler than September. Also, keep in mind that some religious sites require knees and shoulders to be covered. I would only plan to wear shorts while on the ship as I would hate to not be able to enter a religious site based on wearing the wrong attire  In September you could get some nice sea days where you may want your bathing suit also.
If I was going in September I would take some of both summer and fall. What I mean by that is light-weight casual pants/trousers with short sleeve tops, a sweater or light weight jacket and plan to layer based on the weather in port each day. Don't forget a rain poncho, umbrella or rain jacket too, just in case. It poured in Barcelona our first day pre-cruise and we were all so happy to have rain gear of some sort since we planned to walk around the City. In November there were a few chilly mornings which turned out to be very nice warm days where we would have sweaters or jackets that we would take off. Our sea days ended up very windy and somewhat stormy so warmer clothes were used.
Which ports are you going to? Some could be warmer than others. In November Venice was very chilly when the sun went down 
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